A pre-processing strategy for liquid chromatography time-of-flight mass spectrometry metabolic fingerprinting data

Nikoline Juul Nielsen; Giorgio Tomasi; Rasmus John Normand Frandsen; Matilde Bylov Kristensen; John Nielsen; Henriette Giese; Jan H. Christensen

doi:10.1007/s11306-010-0211-1

A pre-processing strategy for liquid chromatography time-of-flight mass spectrometry metabolic fingerprinting data

Nikoline Juul Nielsen, Giorgio Tomasi, Rasmus John Normand Frandsen, Matilde Bylov Kristensen, John Nielsen, Henriette Giese, Jan H. Christensen

6 Citations (Scopus)

Abstract

A series of simple and robust operations for handling large chromatographic time-of-flight mass spectrometry fingerprinting data has been established and applied to data from extracts of Fusarium graminearum genotypes modified in a non-ribosomal peptide synthase gene by over-expression and deletion. It includes importing data into a computing environment by binning the m/z axis; baseline removal; data transformation and compression across retention times. Each sample represented by a total mass spectrum was normalized to unit sum and variables selected by partial least squares discriminant analysis. Finally, principal component analysis was used for identification of high discriminatory power mass-to-charge ratios (m/z's) separating over-expression, wildtype and deletion genotypes. Two compounds exhibiting a positive correlation to the expected levels in different genotypes were identified. The two compounds were represented by m/z 683.5 with retention time of 8.9 min, and m/z's 774.5 and 775.5 with retention time of 14.1 min. This methodology enables extraction of chemical information from large data sets (>10⁸ entries), and provides a starting point for individual optimization in targeting small molecules from metabolomics data.

Original language	English
Journal	Metabolomics
Volume	6
Issue number	3
Pages (from-to)	341-352
Number of pages	12
ISSN	1573-3882
DOIs	https://doi.org/10.1007/s11306-010-0211-1
Publication status	Published - 2010

Keywords

Fingerprinting
Liquid chromatography
Metabolomics
Time-of-flight mass spectrometry

Access to Document

10.1007/s11306-010-0211-1

Cite this

@article{6fae029484cb42fcb63ce0bb95b33d4d,

title = "A pre-processing strategy for liquid chromatography time-of-flight mass spectrometry metabolic fingerprinting data",

abstract = "A series of simple and robust operations for handling large chromatographic time-of-flight mass spectrometry fingerprinting data has been established and applied to data from extracts of Fusarium graminearum genotypes modified in a non-ribosomal peptide synthase gene by over-expression and deletion. It includes importing data into a computing environment by binning the m/z axis; baseline removal; data transformation and compression across retention times. Each sample represented by a total mass spectrum was normalized to unit sum and variables selected by partial least squares discriminant analysis. Finally, principal component analysis was used for identification of high discriminatory power mass-to-charge ratios (m/z's) separating over-expression, wildtype and deletion genotypes. Two compounds exhibiting a positive correlation to the expected levels in different genotypes were identified. The two compounds were represented by m/z 683.5 with retention time of 8.9 min, and m/z's 774.5 and 775.5 with retention time of 14.1 min. This methodology enables extraction of chemical information from large data sets (>108 entries), and provides a starting point for individual optimization in targeting small molecules from metabolomics data.",

keywords = "Fingerprinting, Liquid chromatography, Metabolomics, Time-of-flight mass spectrometry",

author = "Nielsen, {Nikoline Juul} and Giorgio Tomasi and Frandsen, {Rasmus John Normand} and Kristensen, {Matilde Bylov} and John Nielsen and Henriette Giese and Christensen, {Jan H.}",

year = "2010",

doi = "10.1007/s11306-010-0211-1",

language = "English",

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pages = "341--352",

journal = "Metabolomics",

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T1 - A pre-processing strategy for liquid chromatography time-of-flight mass spectrometry metabolic fingerprinting data

AU - Nielsen, Nikoline Juul

AU - Tomasi, Giorgio

AU - Frandsen, Rasmus John Normand

AU - Kristensen, Matilde Bylov

AU - Nielsen, John

AU - Giese, Henriette

AU - Christensen, Jan H.

PY - 2010

Y1 - 2010

N2 - A series of simple and robust operations for handling large chromatographic time-of-flight mass spectrometry fingerprinting data has been established and applied to data from extracts of Fusarium graminearum genotypes modified in a non-ribosomal peptide synthase gene by over-expression and deletion. It includes importing data into a computing environment by binning the m/z axis; baseline removal; data transformation and compression across retention times. Each sample represented by a total mass spectrum was normalized to unit sum and variables selected by partial least squares discriminant analysis. Finally, principal component analysis was used for identification of high discriminatory power mass-to-charge ratios (m/z's) separating over-expression, wildtype and deletion genotypes. Two compounds exhibiting a positive correlation to the expected levels in different genotypes were identified. The two compounds were represented by m/z 683.5 with retention time of 8.9 min, and m/z's 774.5 and 775.5 with retention time of 14.1 min. This methodology enables extraction of chemical information from large data sets (>108 entries), and provides a starting point for individual optimization in targeting small molecules from metabolomics data.

AB - A series of simple and robust operations for handling large chromatographic time-of-flight mass spectrometry fingerprinting data has been established and applied to data from extracts of Fusarium graminearum genotypes modified in a non-ribosomal peptide synthase gene by over-expression and deletion. It includes importing data into a computing environment by binning the m/z axis; baseline removal; data transformation and compression across retention times. Each sample represented by a total mass spectrum was normalized to unit sum and variables selected by partial least squares discriminant analysis. Finally, principal component analysis was used for identification of high discriminatory power mass-to-charge ratios (m/z's) separating over-expression, wildtype and deletion genotypes. Two compounds exhibiting a positive correlation to the expected levels in different genotypes were identified. The two compounds were represented by m/z 683.5 with retention time of 8.9 min, and m/z's 774.5 and 775.5 with retention time of 14.1 min. This methodology enables extraction of chemical information from large data sets (>108 entries), and provides a starting point for individual optimization in targeting small molecules from metabolomics data.

KW - Fingerprinting

KW - Liquid chromatography

KW - Metabolomics

KW - Time-of-flight mass spectrometry

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DO - 10.1007/s11306-010-0211-1

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